BLASTP 2.2.18 [Mar-02-2008]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 0013.0109.p
         (229 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311586|ref|YP_003775678.1| ATP-dependent DNA ligase [Herba...   201   4e-53

>gi|300311586|ref|YP_003775678.1| ATP-dependent DNA ligase
           [Herbaspirillum seropedicae SmR1]
          Length = 856

 Score =  201 bits (511), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 104/228 (45%), Positives = 143/228 (62%), Gaps = 11/228 (4%)

Query: 5   RALPQAID----PD---HPPYLEVAEPLGLLSAAQMNVLEFHTWNGTRTSPTKPDRFIFD 57
           + +P+AID    P+   H  Y+ V +  GL++  QM VLE H W  T  +   PDR +FD
Sbjct: 624 QGMPEAIDTIEVPEGEGHAQYMMVNDVAGLVATVQMGVLELHAWGATGAALNHPDRVVFD 683

Query: 58  LDPGSNVSWAAVQEAATLVRGFLQELGLQSLLKTSGGKGLHILVPLRRQHGWDTVKDFSH 117
           LDP  +V WA V E A LVRG L+E+GL   LKTSGGKGLH++VP+R +H W  VKD++H
Sbjct: 684 LDPADDVPWATVVEGAQLVRGLLKEIGLDCFLKTSGGKGLHVMVPIRPEHDWAVVKDWAH 743

Query: 118 AIATHLAQTLPERFSSKSGSRNRVGRIFLDYIRNGFGATTACAWSLRARPGMGVSVPVSW 177
             A HLA+ LP+RF +K     R G+IF+DY+RN  GATT  A+S+RAR G  VSVP++W
Sbjct: 744 RFAAHLARHLPDRFIAKMSKAARNGKIFIDYLRNAPGATTVVAYSVRARDGAPVSVPITW 803

Query: 178 DELERLQ--SGSQWNISNIHTRLD--RGNAPWSNNSFINQSLTSAMRA 221
           +ELE+ +      + +S +  R+     + PW++     Q LT AM A
Sbjct: 804 EELEQGKGIKADHFRVSTMPARIRSLEQHDPWAHFGQAPQRLTKAMLA 851


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.318    0.133    0.414 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 813,583
Number of extensions: 34579
Number of successful extensions: 78
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 78
Number of HSP's successfully gapped: 1
Length of query: 229
Length of database: 1,619,870
Length adjustment: 82
Effective length of query: 147
Effective length of database: 1,231,600
Effective search space: 181045200
Effective search space used: 181045200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 129 (54.3 bits)